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RSS FeedsMolecules, Vol. 24, Pages 1572: Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS (Molecules)

 
 

21 april 2019 07:00:10

 
Molecules, Vol. 24, Pages 1572: Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS (Molecules)
 




In contrast to sophisticated high-throughput sequencing tools for genomic DNA, analytical tools for comparing secondary structure features between multiple single-stranded DNA sequences are less developed. For single-stranded nucleic acid ligands called aptamers, secondary structure is widely thought to play a pivotal role in driving recognition-based binding activity between an aptamer sequence and its specific target. Here, we employ a competition-based aptamer screening platform called CompELS to identify DNA aptamers for a colloidal target. We then analyze predicted secondary structures of the aptamers and a large population of random sequences to identify sequence features and patterns. Our secondary structure analysis identifies patterns ranging from position-dependent score matrixes of individual structural elements to position-independent consensus domains resulting from global alignment.


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82 viewsCategory: Biochemistry, Chemistry, Molecular Biology
 
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